is there a protocol or tutorial that shows how to use CummerRbound after cuffdiff ? I downloaded all the 14 cuffdiff output files from the analysis in usegalaxy account and uploaded them to my local galaxy and tried to use CummeRBound to these data which shows an error ? It says no CummeRbund was detected even though i installed it through tool shed ?

It sounds as if the tool installation is problematic. Double check that you are using the latest version of the tool wrapper (2015-03-16) and Galaxy release. And be certain to install with managed dependencies (this is the default). If the tool install is still problematic, you can contact the tool authors through the Tool Shed when logged in (menu -> Repository Actions).